Contacts of the helix formed by residues 105 - 116 (chain D) in PDB entry 3I54
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ASP* 3.1 30.9 - - - +
46D ARG* 4.2 18.3 + - - +
83D ILE* 4.3 2.9 - - - -
104D MET* 1.3 76.7 - - - +
106D ARG* 1.3 65.4 + - - +
107D ASP* 3.4 13.6 + - - +
108D ALA* 2.9 26.7 + - - +
109D LEU* 3.1 21.3 + - - +
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Residues in contact with ARG 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 3.1 19.4 + - - +
83D ILE* 3.9 41.8 - - + +
86D PRO* 3.4 28.6 - - - +
105D ASP* 1.3 76.7 - - - +
107D ASP* 1.3 63.7 + - - +
109D LEU* 3.3 3.4 + - + +
110D ARG* 2.9 77.7 + - + +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ASP* 3.3 13.0 + - - +
106D ARG* 1.3 84.4 + - - +
108D ALA* 1.3 57.7 + - - +
110D ARG* 3.2 8.8 + - - +
111D SER* 3.0 32.4 + - - -
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D MET* 3.8 20.6 - - + +
105D ASP* 2.9 21.8 + - - +
107D ASP* 1.3 75.3 - - - +
109D LEU* 1.3 57.7 + - - +
111D SER* 3.4 6.7 + - - +
112D TRP* 2.8 29.9 + - - +
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.8 27.8 - - + -
83D ILE* 3.9 14.4 - - + -
84D PHE* 3.8 23.3 - - + -
104D MET* 3.8 25.5 - - + -
105D ASP 3.1 18.0 + - - +
106D ARG* 3.6 3.8 - - - +
108D ALA* 1.3 77.9 - - - +
110D ARG* 1.3 62.0 + - + +
112D TRP* 3.2 10.9 + - + +
113D ILE* 2.9 53.8 + - + +
119D ILE* 5.1 0.4 - - + -
123D LEU* 4.3 12.8 - - + -
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 5.9 0.5 - - - +
121C GLU* 2.9 46.4 + - + +
83D ILE 5.6 1.0 + - - -
106D ARG* 2.9 70.9 + - + +
107D ASP* 3.8 6.3 - - - +
109D LEU* 1.3 80.6 - - + +
111D SER* 1.3 58.2 + - - +
113D ILE* 3.9 7.4 - - + +
114D ALA* 2.9 28.8 + - - +
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Residues in contact with SER 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP 3.0 16.8 + - - -
108D ALA* 3.8 7.6 - - - -
109D LEU 3.2 0.2 - - - -
110D ARG* 1.3 75.8 - - - +
112D TRP* 1.3 63.0 + - - +
114D ALA* 3.4 7.9 + - - +
115D ASP* 3.0 23.3 + - - +
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Residues in contact with TRP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.8 0.9 - - + -
10D ILE* 2.9 38.1 - - + -
11D PHE* 3.9 14.3 - + - -
22D LEU* 2.9 35.2 + - + +
25D GLN* 6.3 2.2 - - + -
26D LEU* 3.9 30.4 - - + +
49D ILE* 4.4 12.1 - - + -
104D MET* 3.6 35.4 - - + -
108D ALA 2.8 19.2 + - - +
109D LEU* 3.2 15.0 + - + +
111D SER* 1.3 77.3 - - - +
113D ILE* 1.3 57.8 + - - +
115D ASP* 3.2 10.5 + - + +
116D ARG* 3.0 22.0 + - - +
119D ILE* 3.7 27.2 - - + +
123D LEU* 6.6 0.2 - - + -
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 3.7 25.8 - - + -
109D LEU* 2.9 38.9 + - + +
110D ARG* 3.9 7.2 - - + +
112D TRP* 1.3 76.3 - - + +
114D ALA* 1.3 65.5 + - - +
116D ARG 3.0 3.6 - - - +
117D PRO* 2.9 36.0 - - + +
119D ILE* 2.9 42.8 - - + -
120D SER* 3.1 26.2 - - - +
123D LEU* 4.4 5.8 - - + -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 4.8 12.0 - - + +
110D ARG 2.9 18.3 + - - +
111D SER* 3.6 9.0 - - - +
113D ILE* 1.3 77.1 - - - +
115D ASP* 1.3 61.5 + - - +
117D PRO* 4.0 7.7 - - - +
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Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.7 23.4 - - + +
111D SER 3.0 13.2 + - - +
112D TRP* 3.3 16.6 - - + +
113D ILE 3.1 0.2 - - - -
114D ALA* 1.3 79.2 - - - +
116D ARG* 1.3 58.6 + - - +
117D PRO* 3.8 4.0 - - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE 2.9 23.5 + - - -
11D PHE* 3.4 19.9 - - - +
12D GLN* 2.8 46.5 + - - +
13D GLY* 4.0 1.6 - - - +
14D VAL 4.4 14.1 + - - +
22D LEU* 3.7 25.4 - - + -
112D TRP 3.0 5.4 + - - +
113D ILE* 3.0 6.3 - - - +
115D ASP* 1.3 76.1 - - - +
117D PRO* 1.3 68.5 - - + +
118D GLU* 3.1 28.1 + - + +
119D ILE* 3.2 33.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il